The structure of the core of the pyruvate dehydrogenase complex in the mitochondria of pig hearts.
Structure of the Partially-assembled gamma-Tubulin Ring Complex from Pig Brain
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 9g3x
Q-score: 0.281
Xu Y, Munoz-Hernandez H, Krutyholowa R, Marxer F, Cetin F, Wieczorek M
Dev Cell (2024) 59 pp. 3161- [ Pubmed: 39321808 DOI: doi:10.1016/j.devcel.2024.09.002 ]
- Gamma-tubulin ring complex in native pig brain (Complex from Sus scrofa)
- Gamma-tubulin complex component (102 kDa, Protein from Sus scrofa)
- Gamma-tubulin complex component (122 kDa, Protein from Sus scrofa)
- Mitotic spindle organizing protein 1 (8 kDa, Protein from Sus scrofa)
- Gamma-tubulin complex component (76 kDa, Protein from Sus scrofa)
- Tubulin gamma chain (51 kDa, Protein from Sus scrofa)
- Gamma-tubulin complex component 3 (103 kDa, Protein from Sus scrofa)
human co-transcriptional RNA capping enzyme RNGTT-CMTR1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w8f
Q-score: 0.228
Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Human co-transcriptional rna capping enzyme rngtt-cmtr1 (Complex)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Transcription elongation factor, m-rna capping enzyme, cmtr1 (Complex from Homo sapiens)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*gp*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-rna (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
Structure of X18 UFO protomer in complex with F6 Fab VHVL domain
Resolution: 4.05 Å
EM Method: Single-particle
Fitted PDBs: 8gp5
Q-score: 0.422
Niu J, Wang Q, Zhao W, Meng B, Xu Y, Zhang X, Feng Y, Qi Q, Hao Y, Zhang X, Liu Y, Xiang J, Shao Y, Yang B
Nat Commun (2023) 14 pp. 4676-4676 [ Pubmed: 37542068 DOI: doi:10.1038/s41467-023-40321-x ]
- F6 fab vl domain (24 kDa, Protein from Homo sapiens)
- X18 ufo protomer in complex with f6 vhvl domain (Complex from Homo sapiens)
- F6 fab vh domain (25 kDa, Protein from Homo sapiens)
- X18 ufo env protomer (69 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
HIV-1 Env X18 UFO in complex with F6 Fab
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8gpg
Q-score: 0.409
Niu J, Wang Q, Zhao W, Meng B, Xu Y, Zhang X, Feng Y, Qi Q, Hao Y, Zhang X, Liu Y, Xiang J, Shao Y, Yang B
Nat Commun (2023) 14 pp. 4676-4676 [ Pubmed: 37542068 DOI: doi:10.1038/s41467-023-40321-x ]
- Hiv-1 env x18 ufo (Complex from Human immunodeficiency virus 1)
- F6 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Hiv-1 env x18 ufo (69 kDa, Protein from Human immunodeficiency virus 1)
- F6 fab (Complex from Homo sapiens)
- Hiv-1 env x18 ufo in complex with f6 fab (Complex from human)
- F6 fab light chain (24 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
RNA polymerase III pre-initiation complex melting complex 1
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8iue
Q-score: 0.291
Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y
Cell Res (2023) 33 pp. 565-568 [ DOI: doi:10.1038/s41422-023-00819-x Pubmed: 37165065 ]
- Transcription factor (Complex)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase (Complex)
- Dna (Complex)
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 1 (43 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Snrna-activating protein complex subunit 3 (46 kDa, Protein from Homo sapiens)
- Transcription factor iiib 50 kda subunit (46 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc2 (127 kDa, Protein from Homo sapiens)
- Transcription factor tfiiib component b'' homolog (294 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Rna polymerase iii pre-initiation complex melting complex 1 (1 MDa, Complex from Homo sapiens)
- Human gene for u 6 rna (143 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna (74-mer) (143 kDa, DNA from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Snrna-activating protein complex subunit 4 (159 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
The structure of INTAC-PEC complex
Resolution: 4.18 Å
EM Method: Single-particle
Fitted PDBs: 7ycx
Q-score: 0.311
Zheng H, Jin Q, Wang X, Qi Y, Liu W, Ren Y, Zhao D, Xavier Chen F, Cheng J, Chen X, Xu Y
Protein Cell (2023) 14 pp. 698-702 [ Pubmed: 36869814 DOI: doi:10.1093/procel/pwad010 ]
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna/rna (Complex)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Intac (Complex from Sus scrofa)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit (Complex)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Unknown2 (1 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Rna (7 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Intac-pec (Complex from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1,dna-directed rna polymerase ii subunit rpb1, ctd1, ctd2, ctd3, ctd4 (217 kDa, Protein from Homo sapiens)
- Non-template dna (14 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Template dna (14 kDa, DNA from synthetic construct)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
The nucleosome-bound human PBAF complex
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7y8r
Q-score: 0.172
Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y
Nat Commun (2022) 13 pp. 7644-7644 [ Pubmed: 36496390 DOI: doi:10.1038/s41467-022-34859-5 ]
- Bromodomain-containing protein 7 (74 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily b member 1 (44 kDa, Protein from Homo sapiens)
- Phd finger protein 10 (56 kDa, Protein from Homo sapiens)
- Swi/snf complex subunit smarcc2 (133 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily d member 1 (58 kDa, Protein from Homo sapiens)
- Unknown (8 kDa, Protein from Homo sapiens)
- Unknown (1 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (213-mer) (65 kDa, DNA from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Protein polybromo-1 (184 kDa, Protein from Homo sapiens)
- Actb protein (fragment) (41 kDa, Protein from Homo sapiens)
- At-rich interactive domain-containing protein 2 (197 kDa, Protein from Homo sapiens)
- Unkown (1 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3 (15 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e member 1 (46 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Actin-like protein 6a (47 kDa, Protein from Homo sapiens)
- Nucleosome-bound human pbaf complex (Complex from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Transcription activator brg1 (184 kDa, Protein from Homo sapiens)
- Dna (213-mer) (65 kDa, DNA from Homo sapiens)
PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
Resolution: 4.16 Å
EM Method: Single-particle
Fitted PDBs: 8gxs
Q-score: 0.093
Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y
Science (2022) 378 pp. 62-68 [ DOI: doi:10.1126/science.abn8131 Pubmed: 36201575 ]
- Mediator of rna polymerase ii transcription subunit 15 (86 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 25 (78 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 14 (160 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 20 (23 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 30 (20 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Cyclin-dependent kinase 7 (39 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 29 (21 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 9 (16 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 17 (72 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 26 (65 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 1 (41 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 4 (29 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 1 (168 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cyclin-h (37 kDa, Protein from Homo sapiens)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 18 (23 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 6 (28 kDa, Protein from Homo sapiens)
- Dna (162-mer) (46 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 28 (19 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 16 (93 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 10 (15 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 31 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Isoform 2 of mediator of rna polymerase ii transcription subunit 8 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 11 (13 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 21 (15 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Dna (162-mer) (53 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Pic-mediator in complex with +1 nucleosome (t40n) in h-binding state (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 24 (110 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 19 (26 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 7 (27 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Mediator of rna polymerase ii transcription subunit 23 (156 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Mediator of rna polymerase ii transcription subunit 22 (22 kDa, Protein from Homo sapiens)
- Mediator of rna polymerase ii transcription subunit 27 (35 kDa, Protein from Homo sapiens)
- Dna (228-mer) (70 kDa, DNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)